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(-) Description

Title :  RB69 DNA POLYMERASE L415M TERNARY COMPLEX
 
Authors :  S. Xia, J. Wang, W. H. Konigsberg
Date :  04 Feb 13  (Deposition) - 19 Feb 14  (Release) - 10 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Rb69, Dna Polymerase, L415M, Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Xia, M. Wood, M. J. Bradley, E. M. De La Cruz, W. H. Konigsberg
Alteration In The Cavity Size Adjacent To The Active Site O Rb69 Dna Polymerase Changes Its Conformational Dynamics.
Nucleic Acids Res. V. 41 9077 2013
PubMed-ID: 23921641  |  Reference-DOI: 10.1093/NAR/GKT674

(-) Compounds

Molecule 1 - DNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RB69 DNA POLYMERASE
    Gene: 43
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE RB69
    Organism Taxid: 12353
    Synonym: GP43
 
Molecule 2 - DNA (5'- D(*TP*CP*GP*TP*CP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
    Chains: T
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*G)-3')
    Chains: P
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA6Ligand/IonCALCIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:411 , LEU A:412 , THR A:413 , SER A:414 , MET A:415 , TYR A:416 , ARG A:482 , LYS A:560 , ASN A:564 , ASP A:623 , CA A:1002 , CA A:1003 , HOH A:1148 , HOH A:1405 , HOH A:1448 , HOH A:1530 , DG P:115 , DT T:4 , DC T:5BINDING SITE FOR RESIDUE ATP A 1001
2AC2SOFTWAREASP A:411 , LEU A:412 , ASP A:623 , ATP A:1001BINDING SITE FOR RESIDUE CA A 1002
3AC3SOFTWAREASP A:411 , ASP A:623 , ATP A:1001BINDING SITE FOR RESIDUE CA A 1003
4AC4SOFTWAREASN A:505 , ASN A:507 , LYS A:531 , HOH A:1453 , HOH A:1455 , HOH A:1456BINDING SITE FOR RESIDUE CA A 1004
5AC5SOFTWAREGLU A:716 , HOH A:1406 , HOH A:1407 , HOH A:1408BINDING SITE FOR RESIDUE CA A 1005
6AC6SOFTWAREGLU A:116 , HOH A:1199 , HOH A:1490 , HOH A:1491BINDING SITE FOR RESIDUE CA A 1006
7AC7SOFTWAREHOH T:128 , HOH T:129 , HOH T:130BINDING SITE FOR RESIDUE CA P 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J2E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J2E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J2E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J2E)

(-) Exons   (0, 0)

(no "Exon" information available for 4J2E)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:901
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4j2ea1 A:1-375 Exonuclease domain of family B DNA polymerases                                                                                                                                                                                                                                                                                                                         d4j2ea2 A:376-901 Family B DNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeee.....eeeeee....eeeee........eee....eeeeee..hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhh.eeeeeeee...............eeeeeeee....eeeeeee.ee..ee....hhhhhhhhhhhh....hhhhhh.eeeeee.hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeee...ee.hhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee......................ee...eeeeee.hhhhhhhhhhh.hhh.eeee....hhhhhhh..........ee....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee..........eeeee..eeeeeeeee..eeeeeeeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.......ee..ee....hhhhhhhhhhhhhh.............eeeeee..........eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j2e A   1 MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSMYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMF 901
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900 


Chain P from PDB  Type:DNA  Length:13
                                             
                 4j2e P 103 GCGGACTGCTTAG 115
                                   112   


Chain T from PDB  Type:DNA  Length:18
                                                  
                 4j2e T   1 TCGTCTAAGCAGTCCGCG  18
                                    10
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J2E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J2E)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  4j2e
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  DPOL_BPR69 | Q38087
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  2.7.7.7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DPOL_BPR69 | Q38087: 1b1f 1b8h 1clq 1ig9 1ih7 1q9x 1q9y 1qe4 1waf 1wag 1wah 1wai 1waj 2atq 2dtu 2dy4 2oyq 2ozm 2ozs 2p5g 2p5o 3cfo 3cfp 3cfr 3cq8 3kd1 3kd5 3l8b 3lds 3lzi 3lzj 3nae 3nci 3ndk 3ne6 3ngi 3nhg 3qei 3qep 3qer 3qes 3qet 3qev 3qew 3qex 3qnn 3qno 3rma 3rmb 3rmc 3rmd 3rwu 3s9h 3scx 3si6 3sjj 3snn 3spy 3spz 3sq0 3sq1 3sq2 3sq4 3sun 3suo 3sup 3suq 3tab 3tae 3taf 3tag 3uiq 4dtj 4dtm 4dtn 4dto 4dtp 4dtr 4dts 4dtu 4dtx 4du1 4du3 4du4 4e3s 4fj5 4fj7 4fj8 4fj9 4fjg 4fjh 4fji 4fjj 4fjk 4fjl 4fjm 4fjn 4fjx 4fk0 4fk2 4fk4 4i9l 4i9q 4j2a 4j2b 4j2d 4khn 4khq 4khs 4khu 4khw 4khy 4ki4 4ki6 4m3r 4m3t 4m3u 4m3w 4m3x 4m3y 4m3z 4m41 4m42 4m45

(-) Related Entries Specified in the PDB File

4j2a 4j2b 4j2d